Could you post your code for the problem function? It would be interesting to try to reproduce the problem. Pity the die on the core isn't a bit bigger, I could cook some eggs at the same time! 
Just in case it's useful, there's an internal temp sensor on the core's cpu - here's a post that reads it.
Anyone know if the cpu has built in overheat protection? If not, would it be worth adding to the firmware - say, an interrupt that fires regularly, and if temperature sensor indicates overheating a little, the interrupt stalls the cpu to help it cool down, and if overheating a lot, sleeps until the cpu cools to a safer temperature?